Everything else seems to work normally throughout the OS, and with Nisus, but I just tried printing and exporting to PDF (from .rtf), and I get all boxes.

1. This shows in Print Preview, as well as Export.2. This happens only in Nisus (printing in TextEdit prints normally to PDF).3. The boxes are exactly where the font characters should be, including title, indenting. Page numbers show correctly (see sample page upload).4. The bold words even show bold boxes in the right place.

So it's some sort of inability to recognize the font. I've never seen this kind of thing before. Any ideas?

It happens only with a single font -- New Century Schoolbook. It happens with that font also in TextEdit (my first test of TextEdit had a different font, so I didn't see the issue).

NCS is a truetype font, it validates in FontBook, I've printed whole books with it, and it shows as embedded correctly in the PDF output, as reported by Adobe Reader.

And it shows fine in RTF everywhere. But as soon as it hits the Apple PDF engine, ie, in print-preview, it's all boxes and stays that way thereafter.

The font is not new; what's new is that I upgraded the OS from 10.6.8 to 10.11.6, a big jump.

So various possible options. I'll try pulling the font and re-installing it. Then maybe dealing with font caches via the command-line, although I don't operate at sudo level often and I'd rather not in case I break something.

Any other ideas appreciated. This is a favorite font for me and it's necessary for some work-in-progress.

I don't have the font New Century Schoolbook, otherwise I'd check and let you know if I could reproduce the problem too. Is anyone else able to check if their system correctly saves this font to PDF?

You've already listed some good ideas on how to possibly resolve your problem. I think clearing out your font caches is a very good idea, as corrupt font caches have been known to cause these kinds of problems. Please let us know how it goes.

You've already listed some good ideas on how to possibly resolve your problem. I think clearing out your font caches is a very good idea, as corrupt font caches have been known to cause these kinds of problems. Please let us know how it goes.

After a lot of reading online and some dead ends, I appear to have solved it by downloading Fontforge (aside: needs XQuartz to run) and re-saving all four variants (Regular, Bold, etc.) as OpenType (.otf). They were original PS Type 1 fonts. Works now.

I tried overall cache deletion via two methods (command line and safe mode restart), and that didn't help. I could probably have gone further into seeking out font cache files, but my reading lead me to an interesting and somewhat scary set of experiences people had had with the new SIP (System Integrity Protection) causing strange font issues. In particular, I found a detailed explanation of how the SIP keeps a registry in invisible (and SIP protected) files for the name of each font, and how errors at a particular place in the system could make the system think that a version of the font had been introduced by third parties and was therefore illegal. Perhaps that could happen by caches, and perhaps those caches would be invisible files also.

I have no direct evidence that's happened here, but it would take turning off SIP to prove it, and I wasn't ready for that. And besides, if it was invisible caches, then maybe turning off SIP wouldn't solve it anyway if I didn't know where the caches were.

So I decided to rename them. As it turns out, I didn't actually rename them (because then my existing files wouldn't have recognized them) -- just saved them as a different type of font, everything else the same. Which appears to have done the job. No boxes in the OS, or in test PDF file.

I'm very glad you managed to solve this, it sounds like you spent a lot of time on it. It's great you didn't have to touch anything related to SIP. Anything that might further destabilize or even introduce security vulnerabilities into the system should not be taken lightly. Your solution of recreating the bad fonts using a different data format is much safer.

Thanks for updating us and the forum, in case anyone else runs into this problem.

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